Evaluation of post-translational modifications (PTMs):

• Statement (A) is true: Proteolytic cleavage of polyprotein precursors into individual active proteins (e.g., viral polyproteins, insulin precursor) is a major PTM.
• Statement (B) is true: Post-translational hydroxylation of proline and lysine residues by prolyl and lysyl hydroxylases is essential for collagen stability.
• Statement (C) is false: In prokaryotes, formylation of methionine occurs before translation begins on the loaded initiator tRNA ($f\text{Met-tRNA}^{\text{fMet}}$); hence it is a pre-translational event.
• Statement (D) is true: Disulfide bridge formation between cysteine residues occurs post-translationally in the endoplasmic reticulum.

Energetics and cofactor specificity of DNA ligases:

• Assertion (A) is true: The source of free energy required to form the enzyme-AMP intermediate is species-dependent; eubacterial DNA ligases require $\text{NAD}^+$, whereas eukaryotic, archaeal, and phage ligases utilize $\text{ATP}$.
• Reason (R) is false: In E. coli, DNA ligase utilizes $\text{NAD}^+$ (nicotinamide adenine dinucleotide) as its energy cofactor, releasing NMN and AMP, not $\text{ATP}$.
• Therefore, Assertion (A) is true but Reason (R) is false.
• Thus, option 3 is the correct answer.